Multiple sequence alignment - TraesCS6A01G009100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G009100 chr6A 100.000 4091 0 0 1 4091 3775077 3770987 0.000000e+00 7555.0
1 TraesCS6A01G009100 chr6A 88.692 902 69 11 3 884 3801306 3800418 0.000000e+00 1070.0
2 TraesCS6A01G009100 chr6A 86.979 576 63 10 2103 2671 3747034 3746464 4.460000e-179 638.0
3 TraesCS6A01G009100 chr6A 85.900 461 40 14 1547 1995 3747542 3747095 6.190000e-128 468.0
4 TraesCS6A01G009100 chr6A 89.764 127 13 0 1083 1209 3748082 3747956 3.270000e-36 163.0
5 TraesCS6A01G009100 chr6A 97.059 34 1 0 3682 3715 110356530 110356563 1.590000e-04 58.4
6 TraesCS6A01G009100 chr6D 88.204 2594 249 27 1485 4053 4722082 4719521 0.000000e+00 3042.0
7 TraesCS6A01G009100 chr6D 89.483 1103 68 14 81 1137 4723660 4722560 0.000000e+00 1351.0
8 TraesCS6A01G009100 chr6D 82.490 1028 128 31 1484 2487 3713473 3714472 0.000000e+00 854.0
9 TraesCS6A01G009100 chr6D 82.767 795 98 23 2103 2874 3726982 3727760 0.000000e+00 673.0
10 TraesCS6A01G009100 chr6D 87.040 571 63 9 2103 2669 3740051 3740614 5.770000e-178 634.0
11 TraesCS6A01G009100 chr6D 88.010 392 19 8 1124 1488 4722543 4722153 4.850000e-119 438.0
12 TraesCS6A01G009100 chr6D 84.565 460 46 15 1547 1994 3739543 3739989 2.260000e-117 433.0
13 TraesCS6A01G009100 chr6D 79.581 573 88 21 2120 2669 3763844 3764410 2.310000e-102 383.0
14 TraesCS6A01G009100 chr6D 78.822 628 66 20 800 1368 3712567 3713186 1.080000e-95 361.0
15 TraesCS6A01G009100 chr6D 86.577 298 30 8 1698 1994 3726626 3726914 1.830000e-83 320.0
16 TraesCS6A01G009100 chr6D 78.136 590 57 22 686 1209 3756633 3757216 3.970000e-80 309.0
17 TraesCS6A01G009100 chr6D 87.671 146 18 0 1083 1228 3726006 3726151 1.960000e-38 171.0
18 TraesCS6A01G009100 chr6D 88.710 124 14 0 1083 1206 3739061 3739184 7.080000e-33 152.0
19 TraesCS6A01G009100 chr6D 90.000 50 5 0 17 66 4723964 4723915 9.490000e-07 65.8
20 TraesCS6A01G009100 chr6B 87.390 2617 271 29 1484 4085 9034952 9037524 0.000000e+00 2950.0
21 TraesCS6A01G009100 chr6B 92.487 1584 98 10 1485 3058 9058723 9060295 0.000000e+00 2246.0
22 TraesCS6A01G009100 chr6B 85.451 1574 121 42 2 1488 9033332 9034884 0.000000e+00 1539.0
23 TraesCS6A01G009100 chr6B 88.454 1048 101 10 3044 4089 9060355 9061384 0.000000e+00 1247.0
24 TraesCS6A01G009100 chr6B 85.223 582 70 10 2103 2671 9080345 9080923 5.890000e-163 584.0
25 TraesCS6A01G009100 chr6B 88.743 382 34 5 1618 1994 9079906 9080283 3.730000e-125 459.0
26 TraesCS6A01G009100 chr6B 78.374 615 68 23 667 1227 9057537 9058140 5.070000e-89 339.0
27 TraesCS6A01G009100 chrUn 82.347 1031 126 29 1484 2487 306428685 306429686 0.000000e+00 845.0
28 TraesCS6A01G009100 chrUn 78.822 628 66 20 800 1368 306427779 306428398 1.080000e-95 361.0
29 TraesCS6A01G009100 chrUn 88.848 269 23 3 3118 3382 371790579 371790844 1.420000e-84 324.0
30 TraesCS6A01G009100 chr1B 80.212 566 89 20 2116 2671 51106508 51107060 1.770000e-108 403.0
31 TraesCS6A01G009100 chr1B 82.094 363 48 15 1610 1965 51106152 51106504 1.110000e-75 294.0
32 TraesCS6A01G009100 chr1D 83.862 378 48 10 1598 1965 33639270 33639644 8.420000e-92 348.0
33 TraesCS6A01G009100 chr4A 88.476 269 24 3 3118 3382 219304484 219304219 6.600000e-83 318.0
34 TraesCS6A01G009100 chr4A 86.989 269 28 3 3118 3382 310768179 310768444 3.090000e-76 296.0
35 TraesCS6A01G009100 chr3B 86.567 268 28 4 3118 3381 702969561 702969298 5.170000e-74 289.0
36 TraesCS6A01G009100 chr3B 88.983 118 13 0 3118 3235 519146873 519146990 3.300000e-31 147.0
37 TraesCS6A01G009100 chr1A 81.395 387 43 19 1598 1965 32260818 32261194 5.170000e-74 289.0
38 TraesCS6A01G009100 chr7A 90.647 139 13 0 3132 3270 352025649 352025787 6.980000e-43 185.0
39 TraesCS6A01G009100 chr7A 100.000 29 0 0 3684 3712 409881177 409881205 2.000000e-03 54.7
40 TraesCS6A01G009100 chr7D 80.124 161 27 4 3553 3712 370175644 370175488 9.290000e-22 115.0
41 TraesCS6A01G009100 chr2B 85.294 102 15 0 3610 3711 763470510 763470611 5.590000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G009100 chr6A 3770987 3775077 4090 True 7555.000000 7555 100.000000 1 4091 1 chr6A.!!$R1 4090
1 TraesCS6A01G009100 chr6A 3800418 3801306 888 True 1070.000000 1070 88.692000 3 884 1 chr6A.!!$R2 881
2 TraesCS6A01G009100 chr6A 3746464 3748082 1618 True 423.000000 638 87.547667 1083 2671 3 chr6A.!!$R3 1588
3 TraesCS6A01G009100 chr6D 4719521 4723964 4443 True 1224.200000 3042 88.924250 17 4053 4 chr6D.!!$R1 4036
4 TraesCS6A01G009100 chr6D 3712567 3714472 1905 False 607.500000 854 80.656000 800 2487 2 chr6D.!!$F3 1687
5 TraesCS6A01G009100 chr6D 3739061 3740614 1553 False 406.333333 634 86.771667 1083 2669 3 chr6D.!!$F5 1586
6 TraesCS6A01G009100 chr6D 3726006 3727760 1754 False 388.000000 673 85.671667 1083 2874 3 chr6D.!!$F4 1791
7 TraesCS6A01G009100 chr6D 3763844 3764410 566 False 383.000000 383 79.581000 2120 2669 1 chr6D.!!$F2 549
8 TraesCS6A01G009100 chr6D 3756633 3757216 583 False 309.000000 309 78.136000 686 1209 1 chr6D.!!$F1 523
9 TraesCS6A01G009100 chr6B 9033332 9037524 4192 False 2244.500000 2950 86.420500 2 4085 2 chr6B.!!$F1 4083
10 TraesCS6A01G009100 chr6B 9057537 9061384 3847 False 1277.333333 2246 86.438333 667 4089 3 chr6B.!!$F2 3422
11 TraesCS6A01G009100 chr6B 9079906 9080923 1017 False 521.500000 584 86.983000 1618 2671 2 chr6B.!!$F3 1053
12 TraesCS6A01G009100 chrUn 306427779 306429686 1907 False 603.000000 845 80.584500 800 2487 2 chrUn.!!$F2 1687
13 TraesCS6A01G009100 chr1B 51106152 51107060 908 False 348.500000 403 81.153000 1610 2671 2 chr1B.!!$F1 1061

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
341 587 0.391661 AGCAGGTGCCATTACTCACG 60.392 55.000 0.0 0.0 43.38 4.35 F
675 942 1.490490 AGAGTTGGACAAGGCACAAGA 59.510 47.619 0.0 0.0 0.00 3.02 F
2173 3051 0.830648 TGTTCGGGCTTATCCTCCTG 59.169 55.000 0.0 0.0 34.39 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2882 0.812811 GCATCAATCGAGCAGAGGCA 60.813 55.0 13.83 0.0 44.61 4.75 R
2435 3347 1.451067 CGTAGAGGAACCAGACGACT 58.549 55.0 0.00 0.0 35.59 4.18 R
3797 4844 0.267054 AGAGAGGCCCCATGAGATCA 59.733 55.0 0.00 0.0 0.00 2.92 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.486211 GGTAGCTTGAGTCCTAGCCA 58.514 55.000 9.93 0.00 41.12 4.75
121 362 5.878406 ATAACAAGAAGATCTGATCGGGT 57.122 39.130 11.73 0.00 0.00 5.28
206 447 5.395657 CCCTGATCTTACACTGCACATAGAA 60.396 44.000 0.00 0.00 0.00 2.10
298 544 5.602978 AGTTTACGATCATGGGAGGATTACT 59.397 40.000 0.00 0.00 0.00 2.24
341 587 0.391661 AGCAGGTGCCATTACTCACG 60.392 55.000 0.00 0.00 43.38 4.35
406 652 2.558359 GAGCACTGCCACATTTAACCTT 59.442 45.455 0.00 0.00 0.00 3.50
413 659 6.586082 CACTGCCACATTTAACCTTTGATAAC 59.414 38.462 0.00 0.00 0.00 1.89
426 672 5.535030 ACCTTTGATAACTTTCAGGTGGAAC 59.465 40.000 0.00 0.00 34.56 3.62
432 678 4.918810 AACTTTCAGGTGGAACATCAAC 57.081 40.909 0.00 0.00 45.67 3.18
442 688 5.422012 AGGTGGAACATCAACAAGAAAAACT 59.578 36.000 0.00 0.00 45.67 2.66
459 705 6.547510 AGAAAAACTAATCCAGCTGTTGTCTT 59.452 34.615 13.81 1.18 0.00 3.01
471 717 4.756642 AGCTGTTGTCTTGAAATTCGATCA 59.243 37.500 0.00 0.00 0.00 2.92
675 942 1.490490 AGAGTTGGACAAGGCACAAGA 59.510 47.619 0.00 0.00 0.00 3.02
676 943 2.107204 AGAGTTGGACAAGGCACAAGAT 59.893 45.455 0.00 0.00 0.00 2.40
832 1126 5.894653 AGAGAGAAAGAGTGTAAGGTAGGT 58.105 41.667 0.00 0.00 0.00 3.08
896 1190 1.675641 GTGGCCCCATGACTGTGAC 60.676 63.158 0.00 0.00 0.00 3.67
905 1199 2.419713 CCATGACTGTGACTGATCAGGG 60.420 54.545 26.08 9.93 36.76 4.45
915 1209 3.136443 TGACTGATCAGGGACAGTTTGTT 59.864 43.478 26.08 0.56 45.54 2.83
1060 1390 6.591935 TCTTCCCATTGAACCATCTATACAC 58.408 40.000 0.00 0.00 0.00 2.90
1105 1452 4.517453 AGCTAGCTTGGTAGAACTATCTCG 59.483 45.833 12.68 0.00 37.10 4.04
1148 1531 6.013293 ACTCCAAAGGTAGTTAAGATCTTGCT 60.013 38.462 18.47 16.70 0.00 3.91
1217 1668 5.780282 CCTCCTAGGTATATTGATGTCCACA 59.220 44.000 9.08 0.00 0.00 4.17
1243 1720 8.709386 TCAATAGATGCTTCTCAAACTTCTAC 57.291 34.615 5.22 0.00 33.17 2.59
1276 1753 6.981722 AGTTCTTACTTGTGGCCTTTTATTG 58.018 36.000 3.32 0.00 0.00 1.90
1332 1811 7.917505 CAGAACTAATAGATCATTGCCAAAACC 59.082 37.037 0.00 0.00 0.00 3.27
1345 1824 3.008485 TGCCAAAACCAATATTTCCACCC 59.992 43.478 0.00 0.00 0.00 4.61
1385 1976 5.582665 GCATCCAATATAGCTAGTTAGTGCC 59.417 44.000 0.00 0.00 0.00 5.01
1588 2380 5.106038 CGTATGTACAGGTGTCTCCTTGTTA 60.106 44.000 0.33 0.00 45.67 2.41
1591 2383 5.084519 TGTACAGGTGTCTCCTTGTTATCT 58.915 41.667 0.00 0.00 45.67 1.98
1706 2545 5.757320 ACACTCAACATTGTTTCTCTCTCTG 59.243 40.000 0.00 0.00 0.00 3.35
1723 2568 5.660417 TCTCTCTGGCTTAGTTTCATGAGAT 59.340 40.000 0.00 0.00 0.00 2.75
1732 2579 8.239998 GGCTTAGTTTCATGAGATATTAATGGC 58.760 37.037 0.00 0.00 0.00 4.40
2015 2876 7.965107 CACATTTTTCCTTCGAAAAGAGGATAG 59.035 37.037 4.44 0.00 46.07 2.08
2173 3051 0.830648 TGTTCGGGCTTATCCTCCTG 59.169 55.000 0.00 0.00 34.39 3.86
2302 3194 3.342926 AACTGAGCATCCTCCCTCTAT 57.657 47.619 0.00 0.00 37.29 1.98
2568 3494 2.585330 TGTTGGTGTTGATCTGCATGT 58.415 42.857 0.00 0.00 0.00 3.21
2622 3548 3.010027 TGTGATTCAAATGGGGCTCTACA 59.990 43.478 0.00 0.00 0.00 2.74
2642 3568 2.048597 CTCTACCGCAACGCCACA 60.049 61.111 0.00 0.00 0.00 4.17
2681 3622 1.126488 AGGTGGACGATGATGATGCT 58.874 50.000 0.00 0.00 0.00 3.79
2804 3745 1.774110 TGAAGGAAAACAGCTTGGCA 58.226 45.000 0.00 0.00 0.00 4.92
2912 3862 1.137404 GCGTGCACTTAAGCCATGG 59.863 57.895 16.19 7.63 0.00 3.66
2982 3932 3.129287 GTGGGCTTGTGATTTCCACTATG 59.871 47.826 0.00 0.00 45.86 2.23
3099 4123 2.925578 TGCCATTTTCTCATGAAGCG 57.074 45.000 0.00 0.00 33.28 4.68
3178 4206 4.350368 TGTGTCCTTGTTAGAGAATGCA 57.650 40.909 0.00 0.00 0.00 3.96
3206 4234 3.093717 GGATTCGAACCGAGATGCTTA 57.906 47.619 0.00 0.00 37.14 3.09
3225 4253 4.826556 CTTAAGCACTGCTTCCTAAGAGT 58.173 43.478 19.68 0.00 46.77 3.24
3323 4355 5.991328 ATCGTCGATATGCAGAAAATGTT 57.009 34.783 5.79 0.00 0.00 2.71
3328 4360 7.005958 CGTCGATATGCAGAAAATGTTCATAG 58.994 38.462 0.00 0.00 36.09 2.23
3337 4369 8.469200 TGCAGAAAATGTTCATAGAATTTAGGG 58.531 33.333 0.00 0.00 36.09 3.53
3346 4378 9.627123 TGTTCATAGAATTTAGGGAACATTAGG 57.373 33.333 10.64 0.00 39.51 2.69
3347 4379 9.067986 GTTCATAGAATTTAGGGAACATTAGGG 57.932 37.037 0.00 0.00 35.81 3.53
3387 4419 3.205338 TCGTTTGGTAGTATCGATCCGA 58.795 45.455 0.00 0.00 41.13 4.55
3406 4438 5.063204 TCCGACAAAGAACTGATGAAATGT 58.937 37.500 0.00 0.00 0.00 2.71
3438 4470 6.693978 GCGTCTTATAAAGGTTTGTTGTGTTT 59.306 34.615 0.00 0.00 0.00 2.83
3443 4475 3.409026 AAGGTTTGTTGTGTTTTGGCA 57.591 38.095 0.00 0.00 0.00 4.92
3526 4563 3.791245 AGCAAGAACTAGAGTGCATAGC 58.209 45.455 0.00 0.00 39.50 2.97
3533 4570 5.980116 AGAACTAGAGTGCATAGCAATTACG 59.020 40.000 0.00 0.00 41.47 3.18
3546 4583 8.879759 GCATAGCAATTACGCCTATAAAGAATA 58.120 33.333 0.00 0.00 0.00 1.75
3579 4616 2.279073 CCCTAGGCTCCTCGTGGA 59.721 66.667 2.05 6.00 40.69 4.02
3581 4618 2.128507 CCTAGGCTCCTCGTGGACC 61.129 68.421 1.10 9.24 37.46 4.46
3587 4624 1.979155 CTCCTCGTGGACCAGAGCA 60.979 63.158 1.10 1.38 37.46 4.26
3613 4650 1.588082 GCCATCTGTTTGCTGGTGG 59.412 57.895 0.27 0.27 44.66 4.61
3721 4758 2.920912 GGGTGGACTGTCCGGTGA 60.921 66.667 21.15 1.25 40.17 4.02
3735 4772 4.269523 GTGAGCACCAGGCCACCA 62.270 66.667 5.01 0.00 46.50 4.17
3738 4775 4.052518 AGCACCAGGCCACCATCC 62.053 66.667 5.01 0.00 46.50 3.51
3741 4778 1.679977 CACCAGGCCACCATCCTTG 60.680 63.158 5.01 0.00 0.00 3.61
3755 4793 2.750350 CTTGGGTGGCTCCGAGTT 59.250 61.111 0.00 0.00 34.35 3.01
3776 4814 1.001269 TCCGTGATGTCCCTCTCGT 60.001 57.895 0.00 0.00 31.96 4.18
3790 4837 4.314440 TCGTGTGGGTGGCTCTGC 62.314 66.667 0.00 0.00 0.00 4.26
3791 4838 4.624364 CGTGTGGGTGGCTCTGCA 62.624 66.667 0.00 0.00 0.00 4.41
3792 4839 2.980233 GTGTGGGTGGCTCTGCAC 60.980 66.667 0.00 0.00 0.00 4.57
3793 4840 4.269523 TGTGGGTGGCTCTGCACC 62.270 66.667 0.00 0.00 40.60 5.01
3794 4841 4.269523 GTGGGTGGCTCTGCACCA 62.270 66.667 11.36 0.00 42.99 4.17
3795 4842 3.259314 TGGGTGGCTCTGCACCAT 61.259 61.111 11.36 0.00 42.99 3.55
3796 4843 2.753043 GGGTGGCTCTGCACCATG 60.753 66.667 11.36 0.00 42.99 3.66
3797 4844 2.034687 GGTGGCTCTGCACCATGT 59.965 61.111 5.11 0.00 39.95 3.21
3798 4845 2.338015 GGTGGCTCTGCACCATGTG 61.338 63.158 5.11 0.00 39.95 3.21
3804 4851 1.406477 GCTCTGCACCATGTGATCTCA 60.406 52.381 0.00 0.00 35.23 3.27
3848 4895 1.203237 TCTCTCAGGGCCTCTTCAAGT 60.203 52.381 0.95 0.00 0.00 3.16
3868 4915 1.326951 TGTTCGATCTGCCCGGATGA 61.327 55.000 0.73 0.00 0.00 2.92
3903 4951 4.873129 CGGTCGAGCGGTCCATGG 62.873 72.222 28.25 4.97 0.00 3.66
3904 4952 3.458163 GGTCGAGCGGTCCATGGA 61.458 66.667 11.44 11.44 0.00 3.41
3907 4955 3.147595 CGAGCGGTCCATGGAGGA 61.148 66.667 16.81 0.00 46.75 3.71
4048 5096 2.113139 CCCACGCCTGTTTCTGGT 59.887 61.111 0.00 0.00 0.00 4.00
4054 5102 2.644992 CCTGTTTCTGGTTGGCGC 59.355 61.111 0.00 0.00 0.00 6.53
4075 5123 4.452733 GCCGGGTCTTCTCGGGTG 62.453 72.222 2.18 0.00 45.75 4.61
4089 5137 1.009389 CGGGTGCTCTTTGAGTCGTC 61.009 60.000 0.00 0.00 31.39 4.20
4090 5138 0.670854 GGGTGCTCTTTGAGTCGTCC 60.671 60.000 0.00 0.00 31.39 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.815581 ACAAGGAGTATGCAATAAGGAACA 58.184 37.500 0.00 0.00 0.00 3.18
13 14 2.840651 CTCCCCTGACAACAAGGAGTAT 59.159 50.000 0.00 0.00 39.66 2.12
15 16 1.059913 CTCCCCTGACAACAAGGAGT 58.940 55.000 0.00 0.00 39.66 3.85
51 52 1.063114 GGACTCAAGCTACCCCCTAGA 60.063 57.143 0.00 0.00 0.00 2.43
54 55 1.016415 TAGGACTCAAGCTACCCCCT 58.984 55.000 0.00 0.00 0.00 4.79
77 78 2.029073 CTTGTCGGTGAGGCGTGT 59.971 61.111 0.00 0.00 0.00 4.49
121 362 3.244009 GCCTGATCCGATCTCAATCAGAA 60.244 47.826 21.25 0.00 46.01 3.02
206 447 3.654273 TCCCTCTAATTCCTTCCACGAT 58.346 45.455 0.00 0.00 0.00 3.73
298 544 0.535335 GGAGGATGCCGTACAGACAA 59.465 55.000 0.00 0.00 0.00 3.18
341 587 1.004394 CAACTAGGGTCCCCTTTGTCC 59.996 57.143 10.83 0.00 45.70 4.02
406 652 6.303054 TGATGTTCCACCTGAAAGTTATCAA 58.697 36.000 0.00 0.00 33.94 2.57
413 659 4.580167 TCTTGTTGATGTTCCACCTGAAAG 59.420 41.667 0.00 0.00 33.94 2.62
426 672 7.327761 CAGCTGGATTAGTTTTTCTTGTTGATG 59.672 37.037 5.57 0.00 0.00 3.07
432 678 6.507023 ACAACAGCTGGATTAGTTTTTCTTG 58.493 36.000 19.93 10.63 0.00 3.02
442 688 6.348458 CGAATTTCAAGACAACAGCTGGATTA 60.348 38.462 19.93 0.00 0.00 1.75
459 705 5.703978 TTTTGGAGCTTGATCGAATTTCA 57.296 34.783 0.00 0.00 0.00 2.69
485 732 8.475639 ACTTAACCACGACTCATATAATTCTGT 58.524 33.333 0.00 0.00 0.00 3.41
501 748 5.351233 TCAGCAACAATTACTTAACCACG 57.649 39.130 0.00 0.00 0.00 4.94
553 800 2.612972 CCAAGTACAACTCGCAGGTGAT 60.613 50.000 8.00 0.00 33.95 3.06
628 877 7.454066 AGCTCCTGTAAATCATCAGATCAGATA 59.546 37.037 0.00 0.00 31.90 1.98
633 882 7.039784 ACTCTAGCTCCTGTAAATCATCAGATC 60.040 40.741 0.00 0.00 31.90 2.75
832 1126 6.237154 TCATCACAATGGATGACACAAAGTA 58.763 36.000 9.35 0.00 46.46 2.24
879 1173 1.847506 AGTCACAGTCATGGGGCCA 60.848 57.895 4.39 0.00 33.74 5.36
896 1190 5.284079 CAAAAACAAACTGTCCCTGATCAG 58.716 41.667 16.24 16.24 37.65 2.90
905 1199 1.923864 CGGTGGCAAAAACAAACTGTC 59.076 47.619 0.00 0.00 0.00 3.51
915 1209 1.098712 GTGTGACTCCGGTGGCAAAA 61.099 55.000 14.93 2.43 0.00 2.44
1060 1390 4.946478 AGTTAGGATGATTTCTCTCCCG 57.054 45.455 0.00 0.00 0.00 5.14
1105 1452 4.187694 GGAGTTGATGAGGAGATCACAAC 58.812 47.826 0.00 0.00 43.16 3.32
1148 1531 3.636679 CTGAAGAGAGAGACCACCCATA 58.363 50.000 0.00 0.00 0.00 2.74
1217 1668 9.323985 GTAGAAGTTTGAGAAGCATCTATTGAT 57.676 33.333 0.00 0.00 35.54 2.57
1243 1720 6.294010 GGCCACAAGTAAGAACTCTTAAAAGG 60.294 42.308 0.00 1.93 39.84 3.11
1263 1740 9.830975 AAATATGGAAATACAATAAAAGGCCAC 57.169 29.630 5.01 0.00 0.00 5.01
1300 1779 7.255730 GGCAATGATCTATTAGTTCTGGCAAAT 60.256 37.037 10.32 0.00 0.00 2.32
1345 1824 3.068165 TGGATGCTCAGAATACTACCACG 59.932 47.826 0.00 0.00 0.00 4.94
1385 1976 2.404789 GCATCCGTGGTGCAATCG 59.595 61.111 4.51 0.00 42.08 3.34
1396 1987 1.202734 AGGAAGGATCACATGCATCCG 60.203 52.381 15.47 0.00 42.37 4.18
1588 2380 6.490721 GGTACATACTACAGTTAGCCAGAGAT 59.509 42.308 0.00 0.00 0.00 2.75
1591 2383 5.359009 GTGGTACATACTACAGTTAGCCAGA 59.641 44.000 0.00 0.00 44.52 3.86
1706 2545 8.239998 GCCATTAATATCTCATGAAACTAAGCC 58.760 37.037 0.00 0.00 0.00 4.35
1723 2568 0.897863 GCCCCCATGCGCCATTAATA 60.898 55.000 4.18 0.00 0.00 0.98
1748 2600 2.289694 GGTAGAATGTCGGCCTGCATAT 60.290 50.000 0.00 0.72 0.00 1.78
1749 2601 1.070134 GGTAGAATGTCGGCCTGCATA 59.930 52.381 0.00 0.00 0.00 3.14
2021 2882 0.812811 GCATCAATCGAGCAGAGGCA 60.813 55.000 13.83 0.00 44.61 4.75
2173 3051 2.267324 GACAGGAGCAGGGTGAGC 59.733 66.667 0.00 0.00 0.00 4.26
2281 3159 1.963985 AGAGGGAGGATGCTCAGTTT 58.036 50.000 16.72 0.00 0.00 2.66
2302 3194 8.729756 CAATCATGGATCAACAAACTAACACTA 58.270 33.333 0.00 0.00 0.00 2.74
2435 3347 1.451067 CGTAGAGGAACCAGACGACT 58.549 55.000 0.00 0.00 35.59 4.18
2568 3494 1.838112 CCAAGAATGTTGGGCAGCTA 58.162 50.000 0.56 0.00 35.96 3.32
2622 3548 4.078516 GGCGTTGCGGTAGAGGGT 62.079 66.667 0.00 0.00 0.00 4.34
2804 3745 2.125912 GTCTCGTCGCTGGTGCAT 60.126 61.111 0.00 0.00 39.64 3.96
2831 3772 1.380403 CGTGGGTTGCCTTGTCAACA 61.380 55.000 8.60 0.00 45.98 3.33
2886 3836 2.351418 GCTTAAGTGCACGCATACATCA 59.649 45.455 12.01 0.00 0.00 3.07
2982 3932 2.128035 CGAGCATCTAATGGAACGTCC 58.872 52.381 0.00 0.00 36.96 4.79
3078 4102 3.194116 ACGCTTCATGAGAAAATGGCAAT 59.806 39.130 0.00 0.00 32.35 3.56
3099 4123 2.649331 TGCTTCTACTTCCGTGCTAC 57.351 50.000 0.00 0.00 0.00 3.58
3162 4190 2.421424 GTGGCTGCATTCTCTAACAAGG 59.579 50.000 0.50 0.00 0.00 3.61
3178 4206 1.218316 GGTTCGAATCCGAGTGGCT 59.782 57.895 0.00 0.00 46.39 4.75
3225 4253 5.554437 TGGTGAAATTGGTAGACACACTA 57.446 39.130 0.00 0.00 33.82 2.74
3312 4344 8.686334 TCCCTAAATTCTATGAACATTTTCTGC 58.314 33.333 0.00 0.00 32.36 4.26
3323 4355 8.344939 ACCCTAATGTTCCCTAAATTCTATGA 57.655 34.615 0.00 0.00 0.00 2.15
3328 4360 8.129496 TGAAAACCCTAATGTTCCCTAAATTC 57.871 34.615 0.00 0.00 0.00 2.17
3360 4392 4.978186 TCGATACTACCAAACGAAGTCTG 58.022 43.478 0.00 0.00 45.00 3.51
3406 4438 7.653647 ACAAACCTTTATAAGACGCAAATGAA 58.346 30.769 0.00 0.00 0.00 2.57
3420 4452 5.491982 TGCCAAAACACAACAAACCTTTAT 58.508 33.333 0.00 0.00 0.00 1.40
3533 4570 6.817140 CGGGTACTCCAATATTCTTTATAGGC 59.183 42.308 0.00 0.00 34.36 3.93
3579 4616 4.052518 GCCATGGGGTGCTCTGGT 62.053 66.667 15.13 0.00 36.17 4.00
3581 4618 3.369410 ATGGCCATGGGGTGCTCTG 62.369 63.158 20.04 0.00 36.17 3.35
3587 4624 0.615544 CAAACAGATGGCCATGGGGT 60.616 55.000 26.56 15.25 36.17 4.95
3613 4650 3.512516 GTGGCTCCCGATGCAAGC 61.513 66.667 0.00 0.00 35.27 4.01
3721 4758 4.052518 GGATGGTGGCCTGGTGCT 62.053 66.667 3.32 0.00 40.92 4.40
3735 4772 2.285368 TCGGAGCCACCCAAGGAT 60.285 61.111 0.00 0.00 34.64 3.24
3738 4775 1.073199 AAACTCGGAGCCACCCAAG 59.927 57.895 4.58 0.00 34.64 3.61
3741 4778 1.671379 GACAAACTCGGAGCCACCC 60.671 63.158 4.58 0.00 34.64 4.61
3744 4782 2.342279 CGGACAAACTCGGAGCCA 59.658 61.111 4.58 0.00 0.00 4.75
3755 4793 0.895530 GAGAGGGACATCACGGACAA 59.104 55.000 0.00 0.00 0.00 3.18
3793 4840 0.477204 AGGCCCCATGAGATCACATG 59.523 55.000 22.05 22.05 44.78 3.21
3794 4841 0.769873 GAGGCCCCATGAGATCACAT 59.230 55.000 0.00 0.00 0.00 3.21
3795 4842 0.326904 AGAGGCCCCATGAGATCACA 60.327 55.000 0.00 0.00 0.00 3.58
3796 4843 0.396060 GAGAGGCCCCATGAGATCAC 59.604 60.000 0.00 0.00 0.00 3.06
3797 4844 0.267054 AGAGAGGCCCCATGAGATCA 59.733 55.000 0.00 0.00 0.00 2.92
3798 4845 0.686224 CAGAGAGGCCCCATGAGATC 59.314 60.000 0.00 0.00 0.00 2.75
3848 4895 0.461870 CATCCGGGCAGATCGAACAA 60.462 55.000 0.00 0.00 0.00 2.83
3868 4915 2.997897 GGTCGCCAGGGTCTGAGT 60.998 66.667 0.00 0.00 32.44 3.41
3903 4951 3.480133 CCCCCGTGGTCCATCCTC 61.480 72.222 0.00 0.00 37.07 3.71
3938 4986 1.809207 GATGGACAACGCCCAATGG 59.191 57.895 0.00 0.00 37.22 3.16
4061 5109 1.545706 AAGAGCACCCGAGAAGACCC 61.546 60.000 0.00 0.00 0.00 4.46
4070 5118 1.006102 ACGACTCAAAGAGCACCCG 60.006 57.895 0.00 0.00 32.04 5.28


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.